Microorganisms

18 pages, 2841 KiB

Open AccessArticle

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge

by Chenbing Ai, Zhang Yan, Han Zhou, Shanshan Hou, Liyuan Chai, Guanzhou Qiu and Weimin Zeng

Microorganisms 2019, 7(12), 713; https://doi.org/10.3390/microorganisms7120713 - 17 Dec 2019

Cited by 24 | Viewed by 6530

Abstract

It is well acknowledged that the activities of activated sludge (AS) are influenced by seasonal temperature variation. However, the underlying mechanisms remain largely unknown. Here, the activities of activated sludge under three simulated temperature variation trends were compared in lab-scale. The TN, HN [...] Read more.

It is well acknowledged that the activities of activated sludge (AS) are influenced by seasonal temperature variation. However, the underlying mechanisms remain largely unknown. Here, the activities of activated sludge under three simulated temperature variation trends were compared in lab-scale. The TN, HN₃-H, and COD removal activities of activated sludge were improved as temperature elevated from 20 °C to 35 °C. While, the TN, HN₃-H, COD and total phosphorus removal activities of activated sludge were inhibited as temperature declined from 20 °C to 5 °C. Both the extracellular polymer substances (EPS) composition (e.g., total amount, PS, PN and DNA) and sludge index of activated sludge were altered by simulated seasonal temperature variation. The variation of microbial community structures and the functional potentials of activated sludge were further explored by metagenomics. Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla for each activated sludge sample under different temperatures. However, the predominant genera of activated sludge were significantly modulated by simulated temperature variation. The functional genes encoding enzymes for nitrogen metabolism in microorganisms were analyzed. The enzyme genes related to ammonification had the highest abundance despite the changing temperature, especially for gene encoding glutamine synthetase. With the temperature raising from 20 °C to 35 °C. The abundance of amoCAB genes encoding ammonia monooxygenase (EC:1.14.99.39) increased by 305.8%. Meanwhile, all the enzyme genes associate with denitrification were reduced. As the temperature declined from 20 °C to 5 °C, the abundance of enzyme genes related to nitrogen metabolism were raised except for carbamate kinase (EC:2.7.2.2), glutamate dehydrogenase (EC:1.4.1.3), glutamine synthetase (EC:6.3.1.2). Metagenomic data indicate that succession of the dominant genera in microbial community structure is, to some extent, beneficial to maintain the functional stability of activated sludge under the temperature variation within a certain temperature range. This study provides novel insights into the effects of seasonal temperature variation on the activities of activated sludge. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 2140 KiB

Open AccessArticle

Identification of Insect-Deterrent Metabolites from Acremonium masseei strain CICY026, a Saprophytic Fungus from a Sinkhole in Yucatán

by Ana L. Ruiz-Jiménez, Esaú Ruiz-Sánchez, Gabriela Heredia, Raúl Tapia-Tussell, Azucena González-Coloma, Karla Peraza-Jiménez, Felicia A. Moo-Koh, Irma L. Medina-Baizabal, Yanet Hernández-Romero, Gonzalo J. Mena-Rejón, Ramiro F. Quijano-Quiñones and Marcela Gamboa-Angulo

Microorganisms 2019, 7(12), 712; https://doi.org/10.3390/microorganisms7120712 - 17 Dec 2019

Cited by 4 | Viewed by 3435

Abstract

Micromycetes from unexplored sources represent an opportunity to discover novel natural products to control insect pests. With this aim, a strain of Acremonium masseei CICY026 isolated from a tropical sinkhole was identified, cultured on fermented rice, and its ethyl acetate extract (EAE) was [...] Read more.

Micromycetes from unexplored sources represent an opportunity to discover novel natural products to control insect pests. With this aim, a strain of Acremonium masseei CICY026 isolated from a tropical sinkhole was identified, cultured on fermented rice, and its ethyl acetate extract (EAE) was evaluated against three serious phytophagous insects (Bemisia tabaci, Myzus persicae, and Rhopalosiphum padi). DNA from A. masseei CICY026 was used to confirm its identity. EAE caused settling inhibition (SI) of M. persicae and R. padi (67.5% and 75.3%, respectively). Bioassay-guided fractionation of the active EAE led to the isolation of a novel metabolite, named hexahydroacremonintriol (1), and of acremonin A glucoside (2). The structures of 1 and 2 were determined using IR, one- and two-dimensional NMR, HRMS, and confirmed by theoretical data. The aphid M. persicae was noticeably sensitive to 1 and 2 (SI: 55.6% and 67.2%, respectively), whereas R. padi was only slightly affected by 1 (SI: 59%). This new knowledge about mycobiota from these special sinkhole ecosystems will inform the development of new biorational pesticides. Full article

(This article belongs to the Special Issue Yeast and Fungal Metabolites)

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17 pages, 2707 KiB

Open AccessArticle

High Kanamycin Concentration as Another Stress Factor Additional to Temperature to Increase pDNA Production in E. coli DH5α Batch and Fed-Batch Cultures

by Fernando Grijalva-Hernández, Jesús Vega-Estrada, Montserrat Escobar-Rosales, Jaime Ortega-López, Ricardo Aguilar-López, Alvaro R. Lara and Ma. del Carmen Montes-Horcasitas

Microorganisms 2019, 7(12), 711; https://doi.org/10.3390/microorganisms7120711 - 17 Dec 2019

Cited by 6 | Viewed by 6611

Abstract

Plasmid DNA (pDNA) vaccines require high supercoiled-pDNA doses (milligrams) to achieve an adequate immune response. Therefore, processes development to obtain high pDNA yields and productivity is crucial. pDNA production is affected by several factors including culture type, medium composition, and growth conditions. We [...] Read more.

Plasmid DNA (pDNA) vaccines require high supercoiled-pDNA doses (milligrams) to achieve an adequate immune response. Therefore, processes development to obtain high pDNA yields and productivity is crucial. pDNA production is affected by several factors including culture type, medium composition, and growth conditions. We evaluated the effect of kanamycin concentration and temperature on pDNA production, overflow metabolism (organic acids) and metabolic burden (neomycin phosphotransferase II) in batch and fed-batch cultures of Escherichia coli DH5α-pVAX1-NH36. Results indicated that high kanamycin concentration increases the volumetric productivity, volumetric and specific yields of pDNA when batch cultures were carried out at 42 °C, and overflow metabolism reduced but metabolic burden increased. Micrographs taken with a scanning electron microscope (SEM) were analyzed, showing important morphological changes. The high kanamycin concentration (300 mg/L) was evaluated in high cell density culture (50 gDCW/L), which was reached using a fed-batch culture with temperature increase by controlling heating and growth rates. The pDNA volumetric yield and productivity were 759 mg/L and 31.19 mg/L/h, respectively, two-fold greater than the control with a kanamycin concentration of 50 mg/L. A stress-based process simultaneously caused by temperature and high kanamycin concentration can be successfully applied to increase pDNA production. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Biotechnology)

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15 pages, 1036 KiB

Open AccessArticle

Effects of Linoleic Acid on Gut-Derived Bifidobacterium breve DSM 20213: A Transcriptomic Approach

by Alice Senizza, Maria Luisa Callegari, Biancamaria Senizza, Andrea Minuti, Gabriele Rocchetti, Lorenzo Morelli and Vania Patrone

Microorganisms 2019, 7(12), 710; https://doi.org/10.3390/microorganisms7120710 - 17 Dec 2019

Cited by 14 | Viewed by 4110

Abstract

Bacterial production of conjugated linoleic acid (CLA) has recently received great attention because of the potential health benefits of this fatty acid. Linoleic acid (LA) can be converted to CLA by several microorganisms, including bifidobacteria, possibly as a detoxification mechanism to avoid the [...] Read more.

Bacterial production of conjugated linoleic acid (CLA) has recently received great attention because of the potential health benefits of this fatty acid. Linoleic acid (LA) can be converted to CLA by several microorganisms, including bifidobacteria, possibly as a detoxification mechanism to avoid the growth inhibition effect of LA. In the present in vitro study, we investigated the gene expression landscape of the intestinal strain Bifidobacterium breve DSM 20213 when exposed to LA. Transcriptomic analysis using RNA-seq revealed that LA induced a multifactorial stress response in the test strain, including upregulation of genes involved in iron uptake and downregulation of genes involved in sugar and oligopeptide transport. We also observed reduced transcription of genes involved in membrane and pili biosynthesis. The upregulation of iron uptake was not related to any putative ability of LA to chelate Fe²⁺, but was somewhat linked to stress response. Furthermore, we demonstrated that LA increased reactive oxygen species (ROS) production in bacterial cells, activating an oxidative stress response. This response was proved by thioredoxin reductase transcription, and was primarily evident among bacteria cultured in the absence of cysteine. This is the first report of the potential mechanisms involved in bacterial LA transport and stress response in B. breve. Full article

(This article belongs to the Special Issue Host-Gut Microbiota Interactions)

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23 pages, 3550 KiB

Open AccessArticle

Fermented Seeds (“Zgougou”) from Aleppo Pine as a Novel Source of Potentially Probiotic Lactic Acid Bacteria

by Jihen Missaoui, Dalila Saidane, Ridha Mzoughi and Fabio Minervini

Microorganisms 2019, 7(12), 709; https://doi.org/10.3390/microorganisms7120709 - 17 Dec 2019

Cited by 19 | Viewed by 4674

Abstract

Microorganisms inhabiting fermented foods represent the main link between the consumption of this food and human health. Although some fermented food is a reservoir of potentially probiotic microorganisms, several foods are still unexplored. This study aimed at characterizing the probiotic potential of lactic [...] Read more.

Microorganisms inhabiting fermented foods represent the main link between the consumption of this food and human health. Although some fermented food is a reservoir of potentially probiotic microorganisms, several foods are still unexplored. This study aimed at characterizing the probiotic potential of lactic acid bacteria isolated from zgougou, a fermented matrix consisting of a watery mixture of Aleppo pine′s seeds. In vitro methods were used to characterize the safety, survival ability in typical conditions of the gastrointestinal tract, and adherence capacity to surfaces, antimicrobial, and antioxidant activities. Strains belonged to the Lactobacillus plantarum group and Enterococcus faecalis showed no DNase, hemolytic, and gelatinase activities. In addition, their susceptibility to most of the tested antibiotics, satisfied some of the safety prerequisites for their potential use as probiotics. All the strains tolerated low pH, gastrointestinal enzymes, and bile salts. They displayed a good antibacterial activity and antibiofilm formation against 10 reference bacterial pathogens, especially when used as a cell-free supernatant. Furthermore, the lactic acid bacteria (LAB) strains inhibited the growth of Aspergillus flavus and Aspergillus carbonarius. Finally, they had good antioxidant activity, although depending on the strain. Overall, the results of this work highlight that zgougou represents an important reservoir of potentially probiotic LAB. Obviously, future studies should be addressed to confirm the health benefits of the LAB strains. Full article

(This article belongs to the Special Issue Microbial Safety of Fermented Products)

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20 pages, 7290 KiB

Open AccessArticle

Introduction of NGS in Environmental Surveillance for Healthcare-Associated Infection Control

by Manola Comar, Maria D’Accolti, Carolina Cason, Irene Soffritti, Giuseppina Campisciano, Luca Lanzoni, Matteo Bisi, Antonella Volta, Sante Mazzacane and Elisabetta Caselli

Microorganisms 2019, 7(12), 708; https://doi.org/10.3390/microorganisms7120708 - 16 Dec 2019

Cited by 32 | Viewed by 5093

Abstract

The hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care. The monitoring of hospital surfaces is generally addressed by microbial cultural isolation, with some performance limitations. Hence there is [...] Read more.

The hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care. The monitoring of hospital surfaces is generally addressed by microbial cultural isolation, with some performance limitations. Hence there is need to implement environmental surveillance systems using more effective methods. This study aimed to evaluate next-generation sequencing (NGS) technologies for hospital environment microbiome characterization, in comparison with conventional and molecular methods, in an Italian pediatric hospital. Environmental samples included critical surfaces of randomized rooms, surgical rooms, intensive care units and delivery rooms. The resistome of the contaminating population was also evaluated. NGS, compared to other methods, detected with higher sensitivity the environmental bacteria, and was the only method able to detect even unsearched bacteria. By contrast, however, it did not detect mycetes, nor it could distinguish viable from dead bacteria. Microbiological and PCR methods could identify and quantify mycetes, in addition to bacteria, and PCR could define the population resistome. These data suggest that NGS could be an effective method for hospital environment monitoring, especially if flanked by PCR for species identification and resistome characterization, providing a potential tool for the control of HAI transmission. Full article

(This article belongs to the Section Public Health Microbiology)

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17 pages, 1063 KiB

Open AccessReview

Pseudomonas aeruginosa Toxin ExoU as a Therapeutic Target in the Treatment of Bacterial Infections

by Daniel M. Foulkes, Keri McLean, Atikah S. Haneef, David G. Fernig, Craig Winstanley, Neil Berry and Stephen B. Kaye

Microorganisms 2019, 7(12), 707; https://doi.org/10.3390/microorganisms7120707 - 16 Dec 2019

Cited by 41 | Viewed by 6886

Abstract

The opportunistic pathogen Pseudomonas aeruginosa employs the type III secretion system (T3SS) and four effector proteins, ExoS, ExoT, ExoU, and ExoY, to disrupt cellular physiology and subvert the host’s innate immune response. Of the effector proteins delivered by the T3SS, ExoU is the [...] Read more.

The opportunistic pathogen Pseudomonas aeruginosa employs the type III secretion system (T3SS) and four effector proteins, ExoS, ExoT, ExoU, and ExoY, to disrupt cellular physiology and subvert the host’s innate immune response. Of the effector proteins delivered by the T3SS, ExoU is the most toxic. In P. aeruginosa infections, where the ExoU gene is expressed, disease severity is increased with poorer prognoses. This is considered to be due to the rapid and irreversible damage exerted by the phospholipase activity of ExoU, which cannot be halted before conventional antibiotics can successfully eliminate the pathogen. This review will discuss what is currently known about ExoU and explore its potential as a therapeutic target, highlighting some of the small molecule ExoU inhibitors that have been discovered from screening approaches. Full article

(This article belongs to the Special Issue Insights Into The Molecular Pathogenesis of Ocular Infections)

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13 pages, 783 KiB

Open AccessArticle

The Effects of a Microorganisms-Based Commercial Product on the Morphological, Biochemical and Yield of Tomato Plants under Two Different Water Regimes

by Carmen-Simona Inculet, Gabriela Mihalache, Vincenzo Michele Sellitto, Raluca-Maria Hlihor and Vasile Stoleru

Microorganisms 2019, 7(12), 706; https://doi.org/10.3390/microorganisms7120706 - 16 Dec 2019

Cited by 25 | Viewed by 3458

Abstract

The practice of organic agriculture represents an essential requirement for conserving natural resources and for providing the food necessary for a growing population, on a sustainable basis. Tomatoes are considered to be one of the most important crops worldwide. In this context, the [...] Read more.

The practice of organic agriculture represents an essential requirement for conserving natural resources and for providing the food necessary for a growing population, on a sustainable basis. Tomatoes are considered to be one of the most important crops worldwide. In this context, the organic production of tomatoes should be taken into more consideration. The use of microorganisms-based commercial products is an alternative to chemical fertilizers. Anyway, the results of their use are still variable because of various factors. The aim of this study was to test the effect of inoculation with AMF, PGPR and fungi-based products (Rizotech plus^®) on the morphological (length of the plants), biochemical (lycopen, polyphenols, antioxidant activity), and number of fruits and yields of four tomato cultivars (Siriana F1, HTP F1, Minaret F1, Inima de Bou) in two different water regimes used for irrigation (200 m³ or 300 m³ of water/hectare) under a protected area. The results showed that the efficiency of Rizotech plus^® application is dependent on the cultivar and the amount of water used. Also, it was clearly demonstrated that the microorganism inoculation significantly increased the yield of Minaret F1, Siriana F1 and HTP F1 cultivars as compared to the uninoculated plants, regardless of the water amount used in the experiment. Moreover, it was observed that for the irrigation of all four cultivars, inoculated with Rizotech plus^®, a lower amount of water (200 m³·ha⁻¹) can be used to get the same length of plants, number of fruits and yield as in the case of a higher amount of water (300 m³·ha⁻¹). In the case of lycopene, polyphenols and antioxidant activity, the results varied with the cultivar and the water amount used. This study gives new information about the functionality and performance of the microorganisms from Rizotech plus^® product when applied to different tomato cultivars grown in a tunnel, in the condition of two different water regimes, contributing to a better characterization of it and maybe to a more efficient use in agriculture to achieve optimum results. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 2978 KiB

Open AccessArticle

Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity

by H. M. Abdullah Al Masud, Yusuke Yanagi, Takahiro Watanabe, Yoshitaka Sato, Hiroshi Kimura and Takayuki Murata

Microorganisms 2019, 7(12), 705; https://doi.org/10.3390/microorganisms7120705 - 16 Dec 2019

Cited by 12 | Viewed by 3868

Abstract

Epstein-Barr virus (EBV) is a member of the gammaherpesvirinae, which causes infectious mononucleosis and several types of cancer. BBRF2 is an uncharacterized gene of EBV and is expressed during the lytic phase. To evaluate its function, BBRF2-knockout EBV was prepared using bacterial artificial [...] Read more.

Epstein-Barr virus (EBV) is a member of the gammaherpesvirinae, which causes infectious mononucleosis and several types of cancer. BBRF2 is an uncharacterized gene of EBV and is expressed during the lytic phase. To evaluate its function, BBRF2-knockout EBV was prepared using bacterial artificial chromosome (BAC) technology and the CRISPR/Cas9 system. Although viral gene expression, DNA synthesis, and progeny secretion were not affected, the infectivity of progeny viruses was significantly reduced by the disruption of BBRF2. When expressed alone, BBRF2 protein localized to the nucleus and cytoplasm, while the coexpression of an interacting partner, BSRF1, resulted in its relocalization to the cytoplasm. Interestingly, the coexpression of BBRF2 protected BSRF1 from proteasome/ubiquitin-dependent degradation. Therefore, BBRF2, together with BSRF1, augments viral infectivity. Full article

(This article belongs to the Special Issue Epstein–Barr Virus Infection and Associated Diseases)

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12 pages, 1366 KiB

Open AccessArticle

Comparison of Four Commercial Screening Assays for the Detection of bla_KPC, bla_NDM, bla_IMP, bla_VIM, and bla_OXA48 in Rectal Secretion Collected by Swabs

by Francesca Del Bianco, Manuela Morotti, Silvia Zannoli, Giorgio Dirani, Michela Fantini, Maria Federica Pedna, Patrizia Farabegoli and Vittorio Sambri

Microorganisms 2019, 7(12), 704; https://doi.org/10.3390/microorganisms7120704 - 16 Dec 2019

Cited by 11 | Viewed by 3797

Abstract

The spread of carbapenem-resistant Enterobacteriaceae (CRE) has been enabled by the lack of control measures directed at carriers of multidrug-resistant organisms in healthcare settings. Screening patients for asymptomatic colonization on the one hand, and implementation of contact precautions on the other hand, reduces [...] Read more.

The spread of carbapenem-resistant Enterobacteriaceae (CRE) has been enabled by the lack of control measures directed at carriers of multidrug-resistant organisms in healthcare settings. Screening patients for asymptomatic colonization on the one hand, and implementation of contact precautions on the other hand, reduces patient-to-patient transmission. Screening plates represents a relatively low-cost method for isolating CRE from rectal swabs; however, molecular assays have become widely available. This study compared the performance of four commercial molecular platforms in detecting clinically significant carbapenemase genes versus routine screening for CRE. A total of 1015 non-duplicated rectal swabs were cultured on a chromogenic carbapenem-resistant selective medium. All growing Enterobacteriaceae strains were tested for carbapenemase-related genes. The same specimens were processed using the following molecular assays: Allplex™ Entero-DR, Amplidiag^® CarbaR + MCR, AusDiagnostics MT CRE EU, and EasyScreen™ ESBL/CPO. The prevalence of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae detected by swab culture was 2.2%, while organisms producing oxacillinase (OXA)-48 and metallo-β-lactamases were infrequent. The cost of CRE-related infection control precautions, which must be kept in place while waiting for screening results, are significant, so the molecular tests could become cost-competitive, especially when the turnaround time is decreased dramatically. Molecular assays represent a powerful diagnostic tool as they allow the rapid detection of the most clinically relevant carbapenemases. Full article

(This article belongs to the Special Issue Non-Tuberculous Mycobacteria: Emerging Diseases and Health Impacts)

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18 pages, 1812 KiB

Open AccessArticle

Chlamydia trachomatis Whole-Proteome Microarray Analysis of The Netherlands Chlamydia Cohort Study

by Katrin Hufnagel, Bernice Hoenderboom, Christoph Harmel, Juliane K. Rohland, Birgit H.B. van Benthem, Servaas A. Morré and Tim Waterboer

Microorganisms 2019, 7(12), 703; https://doi.org/10.3390/microorganisms7120703 - 16 Dec 2019

Cited by 9 | Viewed by 3061

Abstract

Chlamydia trachomatis (Ct) whole-proteome microarrays were utilized to identify antibody patterns associated with infection; pelvic inflammatory disease (PID), tubal factor infertility, chronic pelvic pain (CPP) and ectopic pregnancy in a subsample of the Netherlands Chlamydia cohort study. Serum pools were analyzed on whole-proteome [...] Read more.

Chlamydia trachomatis (Ct) whole-proteome microarrays were utilized to identify antibody patterns associated with infection; pelvic inflammatory disease (PID), tubal factor infertility, chronic pelvic pain (CPP) and ectopic pregnancy in a subsample of the Netherlands Chlamydia cohort study. Serum pools were analyzed on whole-proteome arrays. The 121 most reactive antigens identified during whole-proteome arrays were selected for further analysis with minimized microarrays that allowed for single sera analysis. From the 232 single sera; 145 (62.5%) serum samples were reactive for at least one antigen. To discriminate between positive and negative serum samples; we created a panel of in total 18 antigens which identified 96% of all microarray positive samples. Antigens CT_858; CT_813 and CT_142 were most reactive. Comparison of antibody reactivity’s among women with and without Ct related sequelae revealed that the reactivity of CT_813 and CT_142 was less common among women with PID compared to women without (29.0% versus 58.6%, p = 0.005 and 25.8% versus 50.6%, p = 0.017 respectively). CT_858 was less common among CPP cases compared to controls (33.3% versus 58.6; p = 0.028). Using a whole-proteome array to select antigens for minimized arrays allows for the identification of novel informative antigens as general infection markers or disease associated antigens Full article

(This article belongs to the Special Issue Chlamydiae and Chlamydia like Bacteria)

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11 pages, 839 KiB

Open AccessArticle

Investigation on Antibiotic-Resistance, Biofilm Formation and Virulence Factors in Multi Drug Resistant and Non Multi Drug Resistant Staphylococcus pseudintermedius

by Gabriele Meroni, Joel F. Soares Filipe, Lorenzo Drago and Piera A. Martino

Microorganisms 2019, 7(12), 702; https://doi.org/10.3390/microorganisms7120702 - 16 Dec 2019

Cited by 48 | Viewed by 4537

Abstract

Staphylococcus pseudintermedius is a commensal bacterium frequently isolated from canine skin and recognized as a zoonotic agent especially for dog-owners. This study focused on (a) the antibiotic-resistance phenotypes; (b) the ability to produce biofilm (slime); and (c) the dissemination of virulence factors in [...] Read more.

Staphylococcus pseudintermedius is a commensal bacterium frequently isolated from canine skin and recognized as a zoonotic agent especially for dog-owners. This study focused on (a) the antibiotic-resistance phenotypes; (b) the ability to produce biofilm (slime); and (c) the dissemination of virulence factors in S. pseudintermedius strains. Seventy-three S. pseudintermedius strains were screened for antibiotic-resistance against 22 different molecules by means of Kirby-Bauer assay. The ability to produce biofilm was investigated using the microtiter plate assay (MtP) and the amplification of icaA and icaD genes. Virulence factors such as cytotoxins (lukI), enterotoxins (seC), and exfoliative toxins (siet, expA, and expB) were evaluated. The antibiotic-resistance profiles revealed 42/73 (57%) multi-drug resistant (MDR) strains and 31/73 (43%) not-MDR. All the MDR strains and 8/31 (27%) of not-MDR resulted in biofilm producers. Leukotoxin LukI was found in 70/73 (96%) of the isolates. Moreover, the enterotoxin gene seC was detected in 47/73 (64%) of the strains. All the isolates carried the siet gene, whereas expA and expB were found in 3/73 (4%) and 5/73 (7%), respectively. In conclusion, S. pseudintermedius should be considered a potential zoonotic and human agent able to carry different virulence determinants and capable of producing biofilm which facilitates horizontal gene transfer. Full article

(This article belongs to the Special Issue Biofilm Implant Related Infections)

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3 pages, 173 KiB

Open AccessEditorial

Editorial for the Special Issue: Foodborne Pathogen Distribution, Ecology, Inactivation, and Methods of Differentiation

by Ross C. Beier, Steven L. Foley and Roger B. Harvey

Microorganisms 2019, 7(12), 701; https://doi.org/10.3390/microorganisms7120701 - 15 Dec 2019

Cited by 2 | Viewed by 2211

Abstract

Foodborne pathogens are a major cause of diarrheal disease throughout the world, and 40% of the foodborne illnesses are observed among children under the age of 5 years [...] Full article

(This article belongs to the Special Issue Foodborne Pathogen Distribution, Ecology, Inactivation and Methods of Differentiation)

18 pages, 2472 KiB

Open AccessArticle

Efficacy of Kombucha Obtained from Green, Oolong, and Black Teas on Inhibition of Pathogenic Bacteria, Antioxidation, and Toxicity on Colorectal Cancer Cell Line

by Thida Kaewkod, Sakunnee Bovonsombut and Yingmanee Tragoolpua

Microorganisms 2019, 7(12), 700; https://doi.org/10.3390/microorganisms7120700 - 14 Dec 2019

Cited by 115 | Viewed by 21242

Abstract

Kombucha tea is a refreshing beverage that is produced from the fermentation of tea leaves. In this study, kombucha tea was prepared using 1% green tea, oolong tea, and black tea, and 10% sucrose with acetic acid bacteria and yeast. The pH values [...] Read more.

Kombucha tea is a refreshing beverage that is produced from the fermentation of tea leaves. In this study, kombucha tea was prepared using 1% green tea, oolong tea, and black tea, and 10% sucrose with acetic acid bacteria and yeast. The pH values of the kombucha tea were found to be in a range of 2.70–2.94 at 15 days of fermentation. The lowest pH value of 2.70 was recorded in the kombucha prepared from black tea. The total acidity of kombucha prepared from black tea was the highest by 16.75 g/L and it was still maintained after heat treatment by boiling and after autoclaved. Six organic acids: glucuronic, gluconic, D-saccharic acid 1,4-lactone, ascorbic, acetic, and succinic acid in kombucha tea were detected by HPLC with the optimization for organic acids detection using isocratic elution buffer with C18 conventional column. The highest level of organic acid was gluconic acid. Kombucha prepared from green tea revealed the highest phenolic content and antioxidation against DPPH radicals by 1.248 and 2.642 mg gallic acid/mL kombucha, respectively. Moreover, pathogenic enteric bacteria: Escherichia coli. E. coli O157:H7. Shigella dysenteriae, Salmonella Typhi, and Vibrio cholera were inhibited by kombucha and heat-denatured kombucha with diameter of the inhibition zones ranged from 15.0 ± 0.0–25.0 ± 0.0 mm. In addition, kombucha prepared from green tea and black tea demonstrated toxicity on Caco-2 colorectal cancer cells. Therefore, kombucha tea could be considered as a potential source of the antioxidation, inhibition of pathogenic enteric bacteria, and toxicity on colorectal cancer cells. Full article

(This article belongs to the Special Issue Natural Alternatives against Bacterial Foodborne Pathogens)

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21 pages, 4497 KiB

Open AccessArticle

Cold Adapted Nitrosospira sp.: A Potential Crucial Contributor of Ammonia Oxidation in Cryosols of Permafrost-Affected Landscapes in Northeast Siberia

by Tina Sanders, Claudia Fiencke, Jennifer Hüpeden, Eva Maria Pfeiffer and Eva Spieck

Microorganisms 2019, 7(12), 699; https://doi.org/10.3390/microorganisms7120699 - 14 Dec 2019

Cited by 16 | Viewed by 4689

Abstract

Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved [...] Read more.

Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols. Full article

(This article belongs to the Special Issue Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria)

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16 pages, 461 KiB

Open AccessArticle

Characterization of Mechanisms Lowering Susceptibility to Flumequine among Bacteria Isolated from Chilean Salmonid Farms

by Christopher Concha, Claudio D. Miranda, Luz Hurtado and Jaime Romero

Microorganisms 2019, 7(12), 698; https://doi.org/10.3390/microorganisms7120698 - 14 Dec 2019

Cited by 8 | Viewed by 2448

Abstract

Despite their great importance for human therapy, quinolones are still used in Chilean salmon farming, with flumequine and oxolinic acid currently approved for use in this industry. The aim of this study was to improve our knowledge of the mechanisms conferring low susceptibility [...] Read more.

Despite their great importance for human therapy, quinolones are still used in Chilean salmon farming, with flumequine and oxolinic acid currently approved for use in this industry. The aim of this study was to improve our knowledge of the mechanisms conferring low susceptibility or resistance to quinolones among bacteria recovered from Chilean salmon farms. Sixty-five isolates exhibiting resistance, reduced susceptibility, or susceptibility to flumequine recovered from salmon farms were identified by their 16S rRNA genes, detecting a high predominance of species belonging to the Pseudomonas genus (52%). The minimum inhibitory concentrations (MIC) of flumequine in the absence and presence of the efflux pump inhibitor (EPI) Phe-Arg-β-naphthylamide and resistance patterns of isolates were determined by a microdilution broth and disk diffusion assays, respectively, observing MIC values ranging from 0.25 to >64 µg/mL and a high level of multi-resistance (96%), mostly showing resistance to florfenicol and oxytetracycline. Furthermore, mechanisms conferring low susceptibility to quinolones mediated by efflux pump activity, quinolone target mutations, or horizontally acquired resistance genes (qepA, oqxA, aac(6′)-lb-cr, qnr) were investigated. Among isolates exhibiting resistance to flumequine (≥16 µg/mL), the occurrence of chromosomal mutations in target protein GyrA appears to be unusual (three out of 15), contrasting with the high incidence of mutations in GyrB (14 out of 17). Bacterial isolates showing resistance or reduced susceptibility to quinolones mediated by efflux pumps appear to be highly prevalent (49 isolates, 75%), thus suggesting a major role of intrinsic resistance mediated by active efflux. Full article

(This article belongs to the Section Environmental Microbiology)

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13 pages, 657 KiB

Open AccessReview

The Potential of Microbial Fuel Cells for Remediation of Heavy Metals from Soil and Water—Review of Application

by Chaolin Fang and Varenyam Achal

Microorganisms 2019, 7(12), 697; https://doi.org/10.3390/microorganisms7120697 - 13 Dec 2019

Cited by 70 | Viewed by 7364

Abstract

The global energy crisis and heavy metal pollution are the common problems of the world. It is noted that the microbial fuel cell (MFC) has been developed as a promising technique for sustainable energy production and simultaneously coupled with the remediation of heavy [...] Read more.

The global energy crisis and heavy metal pollution are the common problems of the world. It is noted that the microbial fuel cell (MFC) has been developed as a promising technique for sustainable energy production and simultaneously coupled with the remediation of heavy metals from water and soil. This paper reviewed the performances of MFCs for heavy metal removal from soil and water. Electrochemical and microbial biocatalytic reactions synergistically resulted in power generation and the high removal efficiencies of several heavy metals in wastewater, such as copper, hexavalent chromium, mercury, silver, thallium. The coupling system of MFCs and microbial electrolysis cells (MECs) successfully reduced cadmium and lead without external energy input. Moreover, the effects of pH and electrode materials on the MFCs in water were discussed. In addition, the remediation of heavy metal-contaminated soil by MFCs were summarized, noting that plant-MFC performed very well in the heavy metal removal. Full article

(This article belongs to the Special Issue The Mechanisms and Applications of Microbial Electrocatalysis)

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14 pages, 1457 KiB

Open AccessArticle

Diversity of Rickettsia in Ticks Collected in Abruzzi and Molise Regions (Central Italy)

by Ilaria Pascucci, Marco Di Domenico, Valentina Curini, Antonio Cocco, Daniela Averaimo, Nicola D’Alterio and Cesare Cammà

Microorganisms 2019, 7(12), 696; https://doi.org/10.3390/microorganisms7120696 - 13 Dec 2019

Cited by 14 | Viewed by 2846

Abstract

Rickettsiae have worldwide occurrence and rickettsiosis are widely recognized as emerging infections in several parts of the world. For decades, it was thought that a single pathogenic tick-borne spotted fever group (SFG), Rickettsia, occurred in each continent. Nowadays, thanks to molecular biology, new [...] Read more.

Rickettsiae have worldwide occurrence and rickettsiosis are widely recognized as emerging infections in several parts of the world. For decades, it was thought that a single pathogenic tick-borne spotted fever group (SFG), Rickettsia, occurred in each continent. Nowadays, thanks to molecular biology, new species of Rickettsia responsible for disease in humans are continuously identified worldwide. In a framework of diagnostic activities of the Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Gaporale” and considering some reports of suspected human clinical cases of rickettsiosis, a survey on ticks collected form animals and humans was carried out with the aim to identify the Rickettsia species circulating in Abruzzi and Molise regions. A total of 603 ticks, previously identified at species level by morphology, pooled into 178 tick samples, were tested by pan-Rickettsia RealTime PCR. DNA from specimens positive for Rickettsia spp. was then sequenced in order to identify the Rickettsia species involved. The highest infection rate was detected in Dermacentor marginatus followed by Ixodes ricinus. The selected targets for this purpose were OmpA and gltA. Rickettsia slovaca, Rickettsia monacensis, Rickettsia massiliae, Rickettsia conorii, Rickettsia aeschlimannii, Rickettsia helvetica, Rickettsia raoultii, and Rickettsia felis – like organisms were identified in this study. These are the first data available in the literature for the circulation of SFG Rickettsia species in the selected geographical area. Results made evidence of high rate of infection in ticks. All Rickettsia species detected have been previously involved in human infection. The diversity of Rickettsia detected, and tick species collected reflects the biodiversity in term of wildlife and environment of the area. An association between Rickettsia species, ticks, and the relationships with vertebrate host species are discussed. Due to the peculiar eco-biology of each Rickettsia species, the use of diagnostic tools able to identify Rickettsia at the species level is thus recommended in order to assess the risk for humans and to elucidate more precise etiological diagnosis in clinical cases. Full article

(This article belongs to the Special Issue Epidemiology of Zoonotic Diseases)

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25 pages, 1861 KiB

Open AccessReview

Protective or Detrimental? Understanding the Role of Host Immunity in Leishmaniasis

by Camila dos Santos Meira and Lashitew Gedamu

Microorganisms 2019, 7(12), 695; https://doi.org/10.3390/microorganisms7120695 - 13 Dec 2019

Cited by 32 | Viewed by 10316

Abstract

The intracellular protozoan parasites of the genus Leishmania are the causative agents of leishmaniasis, a vector-borne disease of major public health concern, estimated to affect 12 million people worldwide. The clinical manifestations of leishmaniasis are highly variable and can range from self-healing localized [...] Read more.

The intracellular protozoan parasites of the genus Leishmania are the causative agents of leishmaniasis, a vector-borne disease of major public health concern, estimated to affect 12 million people worldwide. The clinical manifestations of leishmaniasis are highly variable and can range from self-healing localized cutaneous lesions to life-threatening disseminated visceral disease. Once introduced into the skin by infected sandflies, Leishmania parasites interact with a variety of immune cells, such as neutrophils, monocytes, dendritic cells (DCs), and macrophages. The resolution of infection requires a finely tuned interplay between innate and adaptive immune cells, culminating with the activation of microbicidal functions and parasite clearance within host cells. However, several factors derived from the host, insect vector, and Leishmania spp., including the presence of a double-stranded RNA virus (LRV), can modulate the host immunity and influence the disease outcome. In this review, we discuss the immune mechanisms underlying the main forms of leishmaniasis, some of the factors involved with the establishment of infection and disease severity, and potential approaches for vaccine and drug development focused on host immunity. Full article

(This article belongs to the Special Issue Emerging Vector Borne Infections: A Novel Threat for Global Health)

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13 pages, 5149 KiB

Open AccessReview

Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation

by Georgi Muskhelishvili, Raphaël Forquet, Sylvie Reverchon, Sam Meyer and William Nasser

Microorganisms 2019, 7(12), 694; https://doi.org/10.3390/microorganisms7120694 - 13 Dec 2019

Cited by 12 | Viewed by 3465

Abstract

Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this [...] Read more.

Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this article, we explore the relationship between genomic sequence organization and transcription in the commensal bacterium Escherichia coli and the plant pathogen Dickeya. We argue that, while in E. coli the gradient of DNA thermodynamic stability and gene order along the origin-to-terminus axis represent major organizational features orchestrating temporal gene expression, the genomic sequence organization of Dickeya is more complex, demonstrating extended chromosomal domains of thermodynamically distinct DNA sequences eliciting specific transcriptional responses to various kinds of stress encountered during pathogenic growth. This feature of the Dickeya genome is likely an adaptation to the pathogenic lifestyle utilizing differences in genomic sequence organization for the selective expression of virulence traits. We propose that the coupling of DNA thermodynamic stability and genetic function provides a common organizational principle for the coordinated expression of genes during both normal and pathogenic bacterial growth. Full article

(This article belongs to the Special Issue Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution)

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12 pages, 2628 KiB

Open AccessArticle

Biosynthesis of Amino Acids in Xanthomonas oryzae pv. oryzae Is Essential to Its Pathogenicity

by Ting Li, Zhaohong Zhan, Yunuan Lin, Maojuan Lin, Qingbiao Xie, Yinhua Chen, Chaozu He, Jun Tao and Chunxia Li

Microorganisms 2019, 7(12), 693; https://doi.org/10.3390/microorganisms7120693 - 13 Dec 2019

Cited by 14 | Viewed by 4941

Abstract

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice bacterial blight disease, which causes a large reduction in rice production. The successful interaction of pathogens and plants requires a particular nutrient environment that allows pathogen growth and the initiation [...] Read more.

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of rice bacterial blight disease, which causes a large reduction in rice production. The successful interaction of pathogens and plants requires a particular nutrient environment that allows pathogen growth and the initiation of both pathogen and host responses. Amino acid synthesis is essential for bacterial growth when bacteria encounter amino acid-deficient environments, but the effects of amino acid synthesis on Xoo pathogenicity are unclear. Here, we systemically deleted the essential genes (leuB, leuC, leuD, ilvC, thrC, hisD, trpC, argH, metB, and aspC) involved in the synthesis of different amino acids and analyzed the effects of these mutations on Xoo virulence. Our results showed that leucine, isoleucine, valine, histidine, threonine, arginine, tryptophan, and cysteine syntheses are essential to Xoo infection. We further studied the role of leucine in the interaction between pathogens and hosts and found that leucine could stimulate some virulence-related responses and regulate Xoo pathogenicity. Our findings highlight that amino acids not only act as nutrients for bacterial growth but also play essential roles in the Xoo and rice interaction. Full article

(This article belongs to the Section Plant Microbe Interactions)

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13 pages, 983 KiB

Open AccessArticle

Salivary Biomarkers and Oral Microbial Load in Relation to the Dental Status of Adults with Cystic Fibrosis

by Tamara Pawlaczyk-Kamieńska, Maria Borysewicz-Lewicka and Halina Batura-Gabryel

Microorganisms 2019, 7(12), 692; https://doi.org/10.3390/microorganisms7120692 - 13 Dec 2019

Cited by 16 | Viewed by 3269

Abstract

The mutation of cystic fibrosis transmembrane conductance regulator (CFTR) can modify the physical and chemical properties of saliva, which in turn can affect the oral microflora and oral health in patients with cystic fibrosis (CF). The aim of the study was to examine [...] Read more.

The mutation of cystic fibrosis transmembrane conductance regulator (CFTR) can modify the physical and chemical properties of saliva, which in turn can affect the oral microflora and oral health in patients with cystic fibrosis (CF). The aim of the study was to examine oral health status, salivary properties, and total oral bacteria count in CF adults. Dental status was assessed using the decayed missing filled surfaces (DMF-S) index, and oral clearness using the approximal plaque index (API). The Saliva-Check BUFFER test was used to assess saliva, and real-time polymerase chain reaction (PCR) test to determine the total oral bacteria count. CF patients in comparison to healthy controls showed a higher level of examined clinical indices, higher total oral bacteria count, lower salivary flow rate, lower salivary pH, and increased viscosity. Conclusions: In CF patients, saliva properties, accompanied by insufficient dental care, might be an essential dental caries risk factor. In CF patients, among the etiological factors for dental caries, the bacterial agent seems to be less significant. The frequent and long-term infectious pharmacotherapy can probably explain that. A great deal of the information collected on the oral environment in CF patients, which has helped us understand the etiological conditions for inflammation and infection in this area of the body, indicates that proper dental care can mostly counteract these pathologies. Full article

(This article belongs to the Special Issue Oral Microbiota in Health and Disease)

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13 pages, 1092 KiB

Open AccessReview

The Gut Microbiota in Cardiovascular Disease and Arterial Thrombosis

by Anna Lässiger-Herfurth, Giulia Pontarollo, Alexandra Grill and Christoph Reinhardt

Microorganisms 2019, 7(12), 691; https://doi.org/10.3390/microorganisms7120691 - 13 Dec 2019

Cited by 22 | Viewed by 5272

Abstract

The gut microbiota has emerged as a contributing factor in the development of atherosclerosis and arterial thrombosis. Metabolites from the gut microbiota, such as trimethylamine N-oxide and short chain fatty acids, were identified as messengers that induce cell type-specific signaling mechanisms and immune [...] Read more.

The gut microbiota has emerged as a contributing factor in the development of atherosclerosis and arterial thrombosis. Metabolites from the gut microbiota, such as trimethylamine N-oxide and short chain fatty acids, were identified as messengers that induce cell type-specific signaling mechanisms and immune reactions in the host vasculature, impacting the development of cardiovascular diseases. In addition, microbial-associated molecular patterns drive atherogenesis and the microbiota was recently demonstrated to promote arterial thrombosis through Toll-like receptor signaling. Furthermore, by the use of germ-free mouse models, the presence of a gut microbiota was shown to influence the synthesis of endothelial adhesion molecules. Hence, the gut microbiota is increasingly being recognized as an influencing factor of arterial thrombosis and attempts of dietary pre- or probiotic modulation of the commensal microbiota, to reduce cardiovascular risk, are becoming increasingly significant. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)

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14 pages, 305 KiB

Open AccessReview

d-Amino Acids and Lactic Acid Bacteria

by Jyumpei Kobayashi

Microorganisms 2019, 7(12), 690; https://doi.org/10.3390/microorganisms7120690 - 12 Dec 2019

Cited by 49 | Viewed by 6912

Abstract

Proteins are composed of l-amino acids except for glycine, which bears no asymmetric carbon atom. Accordingly, researchers have studied the function and metabolism of l-amino acids in living organisms but have paid less attention to the presence and roles of their [...] Read more.

Proteins are composed of l-amino acids except for glycine, which bears no asymmetric carbon atom. Accordingly, researchers have studied the function and metabolism of l-amino acids in living organisms but have paid less attention to the presence and roles of their d-enantiomers. However, with the recent developments in analytical techniques, the presence of various d-amino acids in the cells of various organisms and the importance of their roles have been revealed. For example, d-serine (d-Ser) and d-aspartate (d-Asp) act as neurotransmitters and hormone-like substances, respectively, in humans, whereas some kinds of d-amino acids act as a biofilm disassembly factor in bacteria. Interestingly, lactic acid bacteria produce various kinds of d-amino acids during fermentation, and many d-amino acids taste sweet, compared with the corresponding l-enantiomers. The influence of d-amino acids on human health and beauty has been reported in recent years. These facts suggest that the d-amino acids produced by lactic acid bacteria are important in terms of the taste and function of lactic-acid-fermented foods. Against this background, unique d-amino-acid-metabolizing enzymes have been searched for and observed in lactic acid bacteria. This review summarizes and introduces the importance of various d-amino acids in this regard. Full article

(This article belongs to the Special Issue Recent Advances in Applied Microbiology)

12 pages, 1627 KiB

Open AccessArticle

Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis

by Markus Antwerpen, Wolfgang Beyer, Olga Bassy, María Victoria Ortega-García, Juan Carlos Cabria-Ramos, Gregor Grass and Roman Wölfel

Microorganisms 2019, 7(12), 689; https://doi.org/10.3390/microorganisms7120689 - 12 Dec 2019

Cited by 11 | Viewed by 3588

Abstract

The largest phylogenetic lineage known to date of the anthrax pathogen Bacillus anthracis is the wide-spread, so-called Trans-Eurasian clade systematically categorized as the A.Br.008/009 group sharing two defining canonical single-nucleotide polymorphisms (canSNP). In this study, we genome-sequenced a collection of 35 B. anthracis [...] Read more.

The largest phylogenetic lineage known to date of the anthrax pathogen Bacillus anthracis is the wide-spread, so-called Trans-Eurasian clade systematically categorized as the A.Br.008/009 group sharing two defining canonical single-nucleotide polymorphisms (canSNP). In this study, we genome-sequenced a collection of 35 B. anthracis strains of this clade, derived from human infections, animal outbreaks or soil, mostly from European countries isolated between 1936 and 2008. The new data were subjected to comparative chromosomal analysis, together with 75 B. anthracis genomes available in public databases, and the relative placements of these isolates were determined within the global phylogeny of the A.Br.008/009 canSNP group. From this analysis, we have detected 3754 chromosomal SNPs, allowing the assignation of the new chromosomal sequences to established sub-clades, to define new sub-clades, such as two new Spanish, one Bulgarian or one German group(s), or to introduce orphan lineages. SNP-based results were compared with that of a multilocus variable number of tandem repeat analysis (MLVA). This analysis indicated that MLVA typing might provide additional information in cases when genomics yields identical genotypes or shows only minor differences. Introducing the delayed mismatch amplification assay (DMAA) PCR-analysis, we developed a cost-effective method to interrogate for a set of ten phylogenetically informative SNPs within genomes of A.Br.008/009 canSNP clade strains of B. anthracis. By this approach, additional 32 strains could be assigned to five of ten defined clades. Full article

(This article belongs to the Special Issue An Update on Anthrax)

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12 pages, 753 KiB

Open AccessArticle

Activation of a Bovine Mammary Epithelial Cell Line by Ruminant-Associated Staphylococcus aureus is Lineage Dependent

by Jurriaan Hoekstra, Victor P. M. G. Rutten, Theo J. G. M. Lam, Kok P. M. Van Kessel, Mirlin P. Spaninks, J. Arjan Stegeman, Lindert Benedictus and Gerrit Koop

Microorganisms 2019, 7(12), 688; https://doi.org/10.3390/microorganisms7120688 - 12 Dec 2019

Cited by 11 | Viewed by 3347

Abstract

Bovine mastitis is a costly disease to the dairy industry and intramammary infections (IMI) with Staphylococcus aureus are a major cause of mastitis. Staphylococcus aureus strains responsible for mastitis in cattle predominantly belong to ruminant-associated clonal complexes (CCs). Recognition of pathogens by bovine [...] Read more.

Bovine mastitis is a costly disease to the dairy industry and intramammary infections (IMI) with Staphylococcus aureus are a major cause of mastitis. Staphylococcus aureus strains responsible for mastitis in cattle predominantly belong to ruminant-associated clonal complexes (CCs). Recognition of pathogens by bovine mammary epithelial cells (bMEC) plays a key role in activation of immune responsiveness during IMI. However, it is still largely unknown to what extent the bMEC response differs according to S. aureus CC. The aim of this study was to determine whether ruminant-associated S. aureus CCs differentially activate bMEC. For this purpose, the immortalized bMEC line PS was stimulated with S. aureus mastitis isolates belonging to four different clonal complexes (CCs; CC133, CC479, CC151 and CC425) and interleukin 8 (IL-8) release was measured as indicator of activation. To validate our bMEC model, we first stimulated PS cells with genetically modified S. aureus strains lacking (protein A, wall teichoic acid (WTA) synthesis) or expressing (capsular polysaccharide (CP) type 5 or type 8) factors expected to affect S. aureus recognition by bMEC. The absence of functional WTA synthesis increased IL-8 release by bMEC in response to bacterial stimulation compared to wildtype. In addition, bMEC released more IL-8 after stimulation with S. aureus expressing CP type 5 compared to CP type 8 or a strain lacking CP expression. Among the S. aureus lineages, isolates belonging to CC133 induced a significantly stronger IL-8 release from bMEC than isolates from the other CCs, and the IL-8 response to CC479 was higher compared to CC151 and CC425. Transcription levels of IL-8, tumor necrosis factor alpha (TNFα), serum amyloid A3 (SAA3), Toll-like receptor (TLR)-2 and nuclear factor κB (NF-κB) in bMEC after bacterial stimulation tended to follow a similar pattern as IL-8 release, but there were no significant differences between the CCs. This study demonstrates a differential activation of bMEC by ruminant-associated CCs of S. aureus, which may have implications for the severity of mastitis during IMI by S. aureus belonging to these lineages. Full article

(This article belongs to the Special Issue Biology and Pathogenesis of Staphylococcus Infection)

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11 pages, 934 KiB

Open AccessArticle

Transmission Network of Deer-Borne Mycobacterium bovis Infection Revealed by a WGS Approach

by Lorraine Michelet, Cyril Conde, Maxime Branger, Thierry Cochard, Franck Biet and Maria Laura Boschiroli

Microorganisms 2019, 7(12), 687; https://doi.org/10.3390/microorganisms7120687 - 12 Dec 2019

Cited by 5 | Viewed by 3250

Abstract

Bovine tuberculosis (TB) is a zoonotic disease, mainly caused by Mycobacterium bovis. France was declared officially TB free in 2001, however, the disease persists in livestock and wildlife. Among wild animals, deer are particularly susceptible to bovine TB. Here, a whole genome [...] Read more.

Bovine tuberculosis (TB) is a zoonotic disease, mainly caused by Mycobacterium bovis. France was declared officially TB free in 2001, however, the disease persists in livestock and wildlife. Among wild animals, deer are particularly susceptible to bovine TB. Here, a whole genome sequence (WGS) analysis was performed on strains with the same genetic profile—spoligotype SB0121, Multiple Loci VNTR Analysis (MLVA) 6 4 5 3 11 2 5 7—isolated from different types of outbreaks, including from deer or cattle herds, or zoological or hunting parks where the presence of infected deer was a common trait in most of them. The results of the phylogeny based on the SNP calling shows that two sub-clusters co-exist in France, one related to deer bred to be raised as livestock, and the other to hunting parks and zoos. The persistence over almost 30 years of sporadic cases due to strains belonging to these clusters highlights the deficiency in the surveillance of captive wildlife and the need for better monitoring of animals, especially before movement between parks or herds. Full article

(This article belongs to the Special Issue Epidemiology of Zoonotic Diseases)

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11 pages, 591 KiB

Open AccessReview

Pathogenesis and Immune Response Caused by Vector-Borne and Other Viral Infections in a Tupaia Model

by Mohammad Enamul Hoque Kayesh, Md Abul Hashem, Bouchra Kitab and Kyoko Tsukiyama-Kohara

Microorganisms 2019, 7(12), 686; https://doi.org/10.3390/microorganisms7120686 - 12 Dec 2019

Cited by 7 | Viewed by 3428

Abstract

The Tupaia or tree shrew (Tupaia belangeri), a small mammal of the Tupaiidae family, is an increasingly used and promising infection model for virological and immunological research. Recently, sequencing of the Tupaia whole genome revealed that it is more homologous to [...] Read more.

The Tupaia or tree shrew (Tupaia belangeri), a small mammal of the Tupaiidae family, is an increasingly used and promising infection model for virological and immunological research. Recently, sequencing of the Tupaia whole genome revealed that it is more homologous to the genome of humans than of rodents. Viral infections are a global threat to human health, and a complex series of events are involved in the interactions between a virus and the host immune system, which play important roles in the activation of an immune response and the outcome of an infection. Majority of immune response data in viral infections are obtained from studies using animal models that enhance the understanding of host-virus interactions; a proper understanding of these interactions is very important for the development of effective antivirals and prophylactics. Therefore, animal models that are permissive to infection and that recapitulate human disease pathogenesis and immune responses to viral infections are essential. Several studies have shown the permissiveness of Tupaia to a number of important human viral infections in vitro and in vivo without prior adaptation of the viruses; the immune responses and clinical manifestations were comparable to those observed in human infections. Thus, the Tupaia is being utilized and developed as a promising immunocompetent small animal model for viral infection studies. In this review, we focused on the immune responses, mostly innate, during viral infection and pathogenesis in the Tupaia model; we evaluated the interaction between the virus and the components of host resistance, the usefulness of this model for immunopathogenesis studies, and the vaccines and antivirals available. Full article

(This article belongs to the Special Issue Emerging Vector Borne Infections: A Novel Threat for Global Health)

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18 pages, 1767 KiB

Open AccessReview

Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections

by Luciana De Vero, Maria Beatrice Boniotti, Marilena Budroni, Pietro Buzzini, Stefano Cassanelli, Roberta Comunian, Maria Gullo, Antonio F. Logrieco, Ilaria Mannazzu, Rosario Musumeci, Iolanda Perugini, Giancarlo Perrone, Andrea Pulvirenti, Paolo Romano, Benedetta Turchetti and Giovanna Cristina Varese

Microorganisms 2019, 7(12), 685; https://doi.org/10.3390/microorganisms7120685 - 12 Dec 2019

Cited by 41 | Viewed by 12568

Abstract

Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, [...] Read more.

Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs. Full article

(This article belongs to the Special Issue Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest)

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23 pages, 906 KiB

Open AccessArticle

Synergistic Effects of Probiotics and Phytobiotics on the Intestinal Microbiota in Young Broiler Chicken

by Hao Ren, Wilfried Vahjen, Temesgen Dadi, Eva-Maria Saliu, Farshad Goodarzi Boroojeni and Jürgen Zentek

Microorganisms 2019, 7(12), 684; https://doi.org/10.3390/microorganisms7120684 - 11 Dec 2019

Cited by 63 | Viewed by 6515

Abstract

Probiotics and phytobiotics have been studied as in-feed antibiotic alternatives for decades, yet there are no studies on their possible symbiotic effects. In the present study, newly hatched chickens were fed with feeds supplemented either with host-specific Lactobacillus strains (L. agilis and [...] Read more.

Probiotics and phytobiotics have been studied as in-feed antibiotic alternatives for decades, yet there are no studies on their possible symbiotic effects. In the present study, newly hatched chickens were fed with feeds supplemented either with host-specific Lactobacillus strains (L. agilis and L. salivarius), commercial phytobiotics, or combinations of both. After 13 days of life, crops and caecums were analyzed for bacterial composition (16S rDNA sequencing, qPCR) and activity (bacterial metabolites). Crop and caecum samples were also used to study the ex vivo survival of a broiler-derived extended-spectrum beta-lactamase (ESBL) producing Escherichia coli strain. In the crop, combinations of probiotics and phytobiotics, but not their single application, increased the dominance of lactobacilli. The single application of phytobiotics reduced the metabolite concentrations in the crop, but certain combinations synergistically upregulated the metabolites. Changes in the qualitative and quantitative composition of the caecal microbiota were less pronounced than in the crop. Acetate concentrations were significantly lower for phytobiotics or the L. agilis probiotic strain compared to the control group, but the L. salivarius probiotic showed significantly higher acetate concentrations alone or in combination with one phytobiotic. The synergistic effects on the reduction of the ex vivo survival of an ESBL producing E. coli strain in crop or caecum contents were also observed for most combinations. This study shows the beneficial synergistic effects of probiotics and phytobiotics on the intestinal bacterial composition and their metabolic activity in young broilers. The reduced survival of potentially problematic bacteria, such as ESBL-producing E. coli further indicates that combinations of probiotics and phytobiotics may lead to a more enhanced functionality than their individual supplementation. Full article

(This article belongs to the Special Issue Strengthening Mucosal Immunity and the Intestinal Microbiome with Probiotics and Prebiotics)

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